Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression data from malignant gliomas

ABSTRACT: Formalin-fixed, paraffin-embedded (FFPE) samples of varying grade (II-IV) malignant gliomas were measured by Illumina cDNA-mediated Annealing, Selection, extension and ligration (DASL) platform. DASL platform was selected for its specialized design for partially degraded RNA.

ORGANISM(S): Homo sapiens

PROVIDER: GSE54004 | GEO | 2014/02/13

SECONDARY ACCESSION(S): PRJNA238077

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Gene expression data from malignant gliomas

Project description:Formalin-fixed, paraffin-embedded (FFPE) samples of varying grade (II-IV) malignant gliomas were measured by Illumina cDNA-mediated Annealing, Selection, extension and ligration (DASL) platform. DASL platform was selected for its specialized design for partially degraded RNA. Overall mRNA was extracted from FFPE samples using the GoldenGate Assay protocol and hybridized to Illumina BeadChips.

2014-02-13 | E-GEOD-54004 | biostudies-arrayexpress

Potential Prognostic Biomarkers for Bone Metastasis from Hepatocellular Carcinoma

Project description:RNA was extracted from 48 pairs of intratumoral and peritumoral formalin-fixed, paraffin-embedded (FFPE) tissue from hepatocellular carcinoma (HCC) patients with and without bone metastases (BM). The Human Cancer Panel DASL Assay containing 502 cancer-related genes was used to identify novel BM-associated genes. A cDNA-mediated annealing, selection, extension, and ligation assay was performed with an array of 502 known cancer-related genes to identify differentially expressed genes in 96 RNA samples. Total RNA was purified from the tissue specimens using the High Pure RNA Paraffin Kit according to the manufacturer’s protocol. DASL experiments were performed to identify genes that were differentially expressed between the BM and NBM groups of matched intratumoral and peritumoral tissues by using A cDNA-mediated annealing, selection, extension, and ligation assay.

2011-10-27 | E-GEOD-27635 | biostudies-arrayexpress

Potential Prognostic Biomarkers for Bone Metastasis from Hepatocellular Carcinoma

2011-10-28 | GSE27635 | GEO

Gene expression profiling of archival tongue carcinoma and normal tongue tissue (subset)

Project description:RNA extracted from 78 FFPE tongue samples, 62 tongue carcinomas and 16 non-malignant controls, were succesfully analysed using the whole genome DASL array to obtain gene expression profiles. Gene expression profiles were used to identify differentially expressed genes with the ultimate goal of finding out their importance for tongue cancer development and maintenance. Sample were formalin fixed paraffin embedded biopsies taken for diagnostic purposes and had been stored between 1 and 13 years. Because of the general poor quality of RNA from archival samples a special focus were put on its effect on the detected expression levels. 28 tumours and 16 controls with a CTdiff< 5 were selected for differential gene expression analysis. Raw data for only these samples were normalized again. Data for these 44 samples can be found here. Total RNA from formalin fixed paraffin embedded sample was extracted using the High Pure RNA Paraffin Kit according to the manufacturer’s protocol. Quality of FFPE sample were evaluated by comparing how well a kousekeeping gene (TUBA6) could be amplified using q-PCR in each FFPE sample compared to two fresh frozen sample (Ctdiff= CTffpe-Ctff). The DASL platform (cDNA-mediated annealing, selection, extension, and ligation assay) was used together with the whole genome arrays to obtain expression data for 20 818 genes.

2012-05-10 | E-GEOD-34106 | biostudies-arrayexpress

Gene expression profiling of archival tongue carcinoma and normal tongue tissue (all samples)

Project description:RNA extracted from 78 FFPE tongue samples, 62 tongue carcinomas and 16 non-malignant controls, were succesfully analysed using the whole genome DASL array to obtain gene expression profiles. Gene expression profiles were used to identify differentially expressed genes with the ultimate goal of finding out their importance for tongue cancer development and maintenance. Sample were formalin fixed paraffin embedded biopsies taken for diagnostic purposes and had been stored between 1 and 13 years. Because of the general poor quality of RNA from archival samples a special focus were put on its effect on the detected expression levels. 28 tumours and 16 controls with a CTdiff< 5 were selected for differential gene expression analysis. Data for only these sample were normalized again and can be found in seperate data file. Total RNA from formalin fixed paraffin embedded sample was extracted using the High Pure RNA Paraffin Kit according to the manufacturer’s protocol. Quality of FFPE sample were evaluated by comparing how well a kousekeeping gene (TUBA6) could be amplified using q-PCR in each FFPE sample compared to two fresh frozen sample (Ctdiff= CTffpe-Ctff). The DASL platform (cDNA-mediated annealing, selection, extension, and ligation assay) was used together with the whole genome arrays to obtain expression data for 20 818 genes.

2012-05-10 | E-GEOD-34105 | biostudies-arrayexpress

Differential Gene Expression between involved and uninvolved sites of Crohn’s disease: Insights into a Distinctive Pathogenesis Profile

Project description:Our objective was to elucidate patterns of gene expression underlying the progression of CD disease. Surgery biopsies (n=60) were assayed using the Illumina cDNA-mediated Annealing, Selection, Extension, and Ligation (DASL) microarray process specifically designed for use with Formalin-Fixed, Paraffin-Embedded (FFPE) clinical samples. Tissue was sampled in consecutive active involved and uninvolved sites at the same time in individual CD patients, and these samples (CD involved and CD uninvolved) were compared with each other as well as to non-inflammatory bowel disease (non-IBD) healthy controls.

2019-02-20 | GSE95095 | GEO

Gene profiling using archival formalin-fixed paraffin-embedded breast cancer specimens can generate informative microarray data: A comparison with matched fresh fine needle aspiration biopsy samples (FNA samples)

Project description:The Formalin-Fixed Paraffin-Embedded (FFPE) samples on selected breast cancer subtypes (ER+/Her2-, ER+/Her2+, ER-/Her2+, and ER-/Her2-) and their paired fresh fine needle aspirated biopsies (FNA) were investigated. The cases represented different subtypes of breast cancers based on their clinical receptors ER (E) and Her2 (H) status to demonstrate the ability of gene profiles to differentiate these tumors. Compared to FNA specimens, FFPE samples yielded relatively more degraded RNA, and 80% of the samples deemed suitable for cDNA-mediated annealing, selection, extension and ligation (DASL) assay. It is able to demonstrate that gene profiles from FFPE microarrays were reproducible and correlated well with the corresponding gene profiles from FNA microarrays. The gene profiles from both FNA and FFPE could differentiate the four breast cancer subtypes, and the expression levels of corresponding gene set were consistent with qRT-PCR and correlated to the clinical outcomes on published microarray data. It supports the use of FFPE specimens to develop a prognostic tool for breast cancers which can obviate the need for fresh specimens.

2011-06-22 | GSE23385 | GEO

2011-06-22 | GSE23384 | GEO

2011-06-22 | E-GEOD-23384 | biostudies-arrayexpress

Whole genome expression profiling based on paraffin embedded tissue of a large DLBCL cohort

Project description:Gene expression profiling was carried out for RNA extracted from Formalin-fixed, paraffin embedded (FFPE) biopsies for 1311 patients with diffuse large b-cell lymphoma (DLBCL) using the Illumina DASL platform.

2021-07-30 | GSE181063 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data